In [1]:
install.packages("igraph")
library(igraph)

Installing package into 'C:/Users/Shane/Documents/R/win-library/3.6'
(as 'lib' is unspecified)


package 'igraph' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Shane\AppData\Local\Temp\RtmpiybAjp\downloaded_packages

Warning message:
"package 'igraph' was built under R version 3.6.3"

Attaching package: 'igraph'


The following objects are masked from 'package:stats':

    decompose, spectrum


The following object is masked from 'package:base':

    union
In [2]:
g1 <- read.graph("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/AbstractsCovid19.graphml", format="graphml")
In [4]:
library(igraph)
V(g1)

+ 2930/2930 vertices, from 27cd00d:
   [1]    1    2    3    4    5    6    7    8    9   10   11   12   13   14
  [15]   15   16   17   18   19   20   21   22   23   24   25   26   27   28
  [29]   29   30   31   32   33   34   35   36   37   38   39   40   41   42
  [43]   43   44   45   46   47   48   49   50   51   52   53   54   55   56
  [57]   57   58   59   60   61   62   63   64   65   66   67   68   69   70
  [71]   71   72   73   74   75   76   77   78   79   80   81   82   83   84
  [85]   85   86   87   88   89   90   91   92   93   94   95   96   97   98
  [99]   99  100  101  102  103  104  105  106  107  108  109  110  111  112
 [113]  113  114  115  116  117  118  119  120  121  122  123  124  125  126
 [127]  127  128  129  130  131  132  133  134  135  136  137  138  139  140
+ ... omitted several vertices
In [5]:
library(igraph)

nodesofinterest <- c("therapeutic vaccine", "vaccine candidate")

# select the nodes having these names
nodesselection <- V(g1)[label %in% nodesofinterest]
# get their  neighborhood 
egoneighborhood <- ego(g1, order=1, nodes = nodesselection, mode = "all", mindist = 0)

# turn the returned list into a graph
egoselection <- induced_subgraph(g1,unlist(egoneighborhood))

V(egoselection)

+ 739/739 vertices, from 5ea2fcd:
  [1]   1   2   3   4   5   6   7   8   9  10  11  12  13  14  15  16  17  18
 [19]  19  20  21  22  23  24  25  26  27  28  29  30  31  32  33  34  35  36
 [37]  37  38  39  40  41  42  43  44  45  46  47  48  49  50  51  52  53  54
 [55]  55  56  57  58  59  60  61  62  63  64  65  66  67  68  69  70  71  72
 [73]  73  74  75  76  77  78  79  80  81  82  83  84  85  86  87  88  89  90
 [91]  91  92  93  94  95  96  97  98  99 100 101 102 103 104 105 106 107 108
[109] 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126
[127] 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144
[145] 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162
[163] 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180
+ ... omitted several vertices
In [6]:
install.packages("GGally")
library(GGally)

Installing package into 'C:/Users/Shane/Documents/R/win-library/3.6'
(as 'lib' is unspecified)


package 'GGally' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Shane\AppData\Local\Temp\RtmpiybAjp\downloaded_packages

Warning message:
"package 'GGally' was built under R version 3.6.3"
Loading required package: ggplot2

Warning message:
"package 'ggplot2' was built under R version 3.6.3"
Registered S3 method overwritten by 'GGally':
  method from   
  +.gg   ggplot2
In [7]:
install.packages("sna")
library(sna)

Installing package into 'C:/Users/Shane/Documents/R/win-library/3.6'
(as 'lib' is unspecified)


package 'sna' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Shane\AppData\Local\Temp\RtmpiybAjp\downloaded_packages

Warning message:
"package 'sna' was built under R version 3.6.3"
Loading required package: statnet.common

Warning message:
"package 'statnet.common' was built under R version 3.6.3"

Attaching package: 'statnet.common'


The following object is masked from 'package:base':

    order


Loading required package: network

Warning message:
"package 'network' was built under R version 3.6.3"
network: Classes for Relational Data
Version 1.16.0 created on 2019-11-30.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.



Attaching package: 'network'


The following objects are masked from 'package:igraph':

    %c%, %s%, add.edges, add.vertices, delete.edges, delete.vertices,
    get.edge.attribute, get.edges, get.vertex.attribute, is.bipartite,
    is.directed, list.edge.attributes, list.vertex.attributes,
    set.edge.attribute, set.vertex.attribute


sna: Tools for Social Network Analysis
Version 2.5 created on 2019-12-09.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
 For citation information, type citation("sna").
 Type help(package="sna") to get started.



Attaching package: 'sna'


The following objects are masked from 'package:igraph':

    betweenness, bonpow, closeness, components, degree, dyad.census,
    evcent, hierarchy, is.connected, neighborhood, triad.census
In [8]:
library(network)
library(intergraph)

ggnet2(egoselection, mode = 'fruchtermanreingold', node.size="weightlinks", node.color = "cluster", label = "label", label.size=2.5, palette="Dark2", alpha = 0.75, edge.alpha = 0.2, size.legend = NULL, size.min = 1000) + theme(legend.position = "none")

Error in library(intergraph): there is no package called 'intergraph'
Traceback:

1. library(intergraph)
In [9]:
install.packages("sigmajs")
library(sigmajs)

Installing package into 'C:/Users/Shane/Documents/R/win-library/3.6'
(as 'lib' is unspecified)


package 'sigmajs' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Shane\AppData\Local\Temp\RtmpiybAjp\downloaded_packages

Warning message:
"package 'sigmajs' was built under R version 3.6.3"
Welcome to sigmajs

Docs: sigmajs.john-coene.com
In [10]:
reducedgraph <- "https://raw.githubusercontent.com/mdurazob/covidnotebook/master/VaccineGraphReduced.gexf"

vaccineInteractive <- sigmajs() %>% 
  sg_from_gexf(reducedgraph) %>% 
  sg_settings(drawLabels = TRUE, drawEdges = FALSE, labelThreshold = 4, labelSize = 10)

vaccineInteractive
In [11]:
library(sigmajs)

cluster1graph <- "https://raw.githubusercontent.com/mdurazob/covidnotebook/master/Cluster1.gexf"

cluster1interactive <- sigmajs() %>% 
  sg_from_gexf(cluster1graph) %>% 
  sg_settings(drawLabels = TRUE, drawEdges = FALSE, labelThreshold = 4, labelSize = 10)

cluster1interactive
In [12]:
install.packages("networkD3")
## Installing package into '/usr/local/lib/R/site-library'
## (as 'lib' is unspecified)

Installing package into 'C:/Users/Shane/Documents/R/win-library/3.6'
(as 'lib' is unspecified)


package 'networkD3' successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\Shane\AppData\Local\Temp\RtmpiybAjp\downloaded_packages
In [14]:
library(networkD3)
edges <- read.csv(file ="https://raw.githubusercontent.com/mdurazob/covidnotebook/master/edgescluster1.csv")
nodes <- read.csv(file = "https://raw.githubusercontent.com/mdurazob/covidnotebook/master/nodescluster1.csv")

d <- sankeyNetwork(Links = edges, Nodes = nodes, Source = "Source", Target = "Target", 
                NodeID = "name", Value = "Weight", # LinkGroup = "colour", (use if you want to colour edges)
                fontSize = 14, fontFamily = "sans-serif", width = "100%")

d
In [15]:
install.packages("highcharter")
library(highcharter)

Installing package into 'C:/Users/Shane/Documents/R/win-library/3.6'
(as 'lib' is unspecified)

also installing the dependencies 'XML', 'data.table', 'stringi', 'generics', 'reshape2', 'TTR', 'curl', 'rlist', 'zoo', 'stringr', 'broom', 'xts', 'quantmod', 'tidyr', 'lubridate', 'whisker'



  There is a binary version available but the source version is later:
         binary source needs_compilation
reshape2  1.4.3  1.4.4              TRUE

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Warning message:
"package 'highcharter' was built under R version 3.6.3"
Registered S3 method overwritten by 'quantmod':
  method            from
  as.zoo.data.frame zoo 

Highcharts (www.highcharts.com) is a Highsoft software product which is

not free for commercial and Governmental use


Attaching package: 'highcharter'


The following object is masked from 'package:networkD3':

    JS
In [16]:
inhibitionpapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/InhibitionPapers.csv")
inhibitionchart <- inhibitionpapers %>% 
hchart('bubble', hcaes(x = 'Name', y = 'Year', size = 'Citations', color='Year')) %>% 
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}")

Warning message:
"`parse_quosure()` is deprecated as of rlang 0.2.0.
Please use `parse_quo()` instead.
This warning is displayed once per session."
Warning message:
"`as_data_frame()` is deprecated as of tibble 2.0.0.
Please use `as_tibble()` instead.
The signature and semantics have changed, see `?as_tibble`.
This warning is displayed once every 8 hours.
Call `lifecycle::last_warnings()` to see where this warning was generated."
In [17]:
library(highcharter)
install.packages("treemap")

Installing package into 'C:/Users/Shane/Documents/R/win-library/3.6'
(as 'lib' is unspecified)

also installing the dependency 'gridBase'



package 'gridBase' successfully unpacked and MD5 sums checked
package 'treemap' successfully unpacked and MD5 sums checked

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In [18]:
library(treemap)
install.packages("viridis")

Warning message:
"package 'treemap' was built under R version 3.6.3"
Installing package into 'C:/Users/Shane/Documents/R/win-library/3.6'
(as 'lib' is unspecified)

also installing the dependency 'gridExtra'



package 'gridExtra' successfully unpacked and MD5 sums checked
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In [19]:
library(viridis)

Warning message:
"package 'viridis' was built under R version 3.6.3"
Loading required package: viridisLite

Warning message:
"package 'viridisLite' was built under R version 3.6.3"
In [20]:
install.packages("RColorBrewer")

Installing package into 'C:/Users/Shane/Documents/R/win-library/3.6'
(as 'lib' is unspecified)


package 'RColorBrewer' successfully unpacked and MD5 sums checked

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In [22]:
library(RColorBrewer)

adepapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/ADEPapers.csv")

hchart(adepapers, "treemap", hcaes(x = Name, value = Citations, color = Year))%>% 
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}") %>% 
  hc_colorAxis(minColor = brewer.pal(9, "Greens")[4],
               maxColor = brewer.pal(9, "Blues")[9])
In [23]:
library(highcharter)
animalmodelspapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/AnimalModelsPapers.csv")

animalmodelschart <- animalmodelspapers %>% 
hchart('bubble', hcaes(x = 'Name', y = 'Year', size = 'Citations', color='Year')) %>% 
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}") 

animalmodelschart
In [24]:
library(highcharter)
library(treemap)
library(viridis)
library(RColorBrewer)

therapeuticspapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/therapeuticspapers.csv")

hchart(therapeuticspapers, "treemap", hcaes(x = Name, value = Citations, color = Year))%>% 
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}") %>% 
  hc_colorAxis(minColor = brewer.pal(9, "Greens")[4],
               maxColor = brewer.pal(9, "Blues")[9])
In [25]:
library(highcharter)
economicspapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/economicsPapers.csv")

economicschart <- economicspapers %>% 
hchart('bubble', hcaes(x = 'Name', y = 'Year', size = 'Citations', color='Year')) %>% 
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}") 

economicschart
In [26]:
library(highcharter)
library(treemap)
library(viridis)
library(RColorBrewer)

standarizationpapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/AnimalStandardized.csv")

hchart(standarizationpapers, "treemap", hcaes(x = Name, value = Citations, color = Year))%>% 
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}") %>% 
  hc_colorAxis(minColor = brewer.pal(9, "Greens")[4],
               maxColor = brewer.pal(9, "Blues")[9])
In [27]:
library(highcharter)
prophylaxispapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/prophylaxispapers.csv")

prophylaxischart <- prophylaxispapers %>% 
hchart('bubble', hcaes(x = 'Name', y = 'Year', size = 'Citations', color='Year')) %>% 
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}") 

prophylaxischart
In [28]:
library(highcharter)
library(treemap)
library(viridis)
library(RColorBrewer)

aftervaccinepapers <- read.csv("https://raw.githubusercontent.com/mdurazob/covidnotebook/master/aftervaccinepapers.csv")

hchart(aftervaccinepapers, "treemap", hcaes(x = Name, value = Citations, color = Year))%>% 
hc_tooltip(pointFormat = "<b>Title: {point.Title}</b><br> <b>Keyword: {point.Name}</b><br> Fragment: {point.Abstract}") %>% 
  hc_colorAxis(minColor = brewer.pal(9, "Greens")[4],
               maxColor = brewer.pal(9, "Blues")[9])
In [ ]: